From 9a79f0355021367a8fd3356709b202761db9f34d Mon Sep 17 00:00:00 2001
From: John Omotani <john.omotani@ukaea.uk>
Date: Tue, 8 Oct 2024 14:36:16 +0100
Subject: [PATCH 1/7] Remove HDF5_jll pinning
Now that NCDatasets is an optional dependency (coupled using an
'extension'), we do not need to use an old version of the HDF5 library
provided by Julia, `HDF5_jll` (cf issue #148). Using the latest version
will allow us to activate parallel I/O in the Github Actions CI jobs.
---
moment_kinetics/Project.toml | 2 --
1 file changed, 2 deletions(-)
diff --git a/moment_kinetics/Project.toml b/moment_kinetics/Project.toml
index fc61043c9a..be7d4b7a42 100644
--- a/moment_kinetics/Project.toml
+++ b/moment_kinetics/Project.toml
@@ -11,7 +11,6 @@ FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838"
Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
-HDF5_jll = "0234f1f7-429e-5d53-9886-15a909be8d59"
Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
LegendrePolynomials = "3db4a2ba-fc88-11e8-3e01-49c72059a882"
LibGit2 = "76f85450-5226-5b5a-8eaa-529ad045b433"
@@ -50,7 +49,6 @@ file_io_netcdf = "NCDatasets"
manufactured_solns_ext = ["Symbolics", "IfElse"]
[compat]
-HDF5_jll = "<1.14, >=1.15"
julia = "1.9.0"
[extras]
From 04015c1ab50b651d159389411f2aa9f0bc6c8223 Mon Sep 17 00:00:00 2001
From: John Omotani <john.omotani@ukaea.uk>
Date: Tue, 8 Oct 2024 14:40:49 +0100
Subject: [PATCH 2/7] Disable "parallel_io" in Harrison-Thompson test
Is good to have a couple of tests that us `parallel_io=false` (the
restart interpolation already did), so that even when parallel I/O is
available, the branch that does not use it gets tested.
---
moment_kinetics/test/harrisonthompson.jl | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/moment_kinetics/test/harrisonthompson.jl b/moment_kinetics/test/harrisonthompson.jl
index 990db4c9d6..d0ec7f31bb 100644
--- a/moment_kinetics/test/harrisonthompson.jl
+++ b/moment_kinetics/test/harrisonthompson.jl
@@ -83,7 +83,8 @@ test_input_finite_difference = Dict("composition" => OptionsDict("n_ion_species"
"upar_phase" => 0.0,
"temperature_amplitude" => 0.0,
"temperature_phase" => 0.0),
- "output" => OptionsDict("run_name" => "finite_difference"),
+ "output" => OptionsDict("run_name" => "finite_difference",
+ "parallel_io" => false),
"evolve_moments" => OptionsDict("density" => false,
"parallel_flow" => false,
"parallel_pressure" => false,
From 331b9fa81e59de02e63094bc2287d96ab8e0cfc2 Mon Sep 17 00:00:00 2001
From: John Omotani <john.omotani@ukaea.uk>
Date: Tue, 8 Oct 2024 14:54:01 +0100
Subject: [PATCH 3/7] Install NCDatasets for the Github Actions CI parallel
checks
NCDatasets was already included for the serial tests. Now that we use
the Julia-provided MPI for the parallel tests, it is also possible to
install NCDatasets for the parallel tests.
---
.github/workflows/debug_checks.yml | 2 +-
.github/workflows/parallel_test.yml | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/.github/workflows/debug_checks.yml b/.github/workflows/debug_checks.yml
index 451c08502f..53c06decf2 100644
--- a/.github/workflows/debug_checks.yml
+++ b/.github/workflows/debug_checks.yml
@@ -28,7 +28,7 @@ jobs:
sed -i -e "s/_debug_level = get_options.*/_debug_level = 2/" moment_kinetics/src/debugging.jl
touch Project.toml
- julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.add(["MPI", "MPIPreferences", "PackageCompiler", "Symbolics"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
+ julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.add(["MPI", "MPIPreferences", "PackageCompiler", "NCDatasets", "Symbolics"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
julia --project -O3 --check-bounds=no -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'
julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.develop(path="moment_kinetics/"); Pkg.precompile()'
julia --project -O3 --check-bounds=yes precompile-with-check-bounds.jl --debug 2
diff --git a/.github/workflows/parallel_test.yml b/.github/workflows/parallel_test.yml
index b3eed45e6b..5441dcc82f 100644
--- a/.github/workflows/parallel_test.yml
+++ b/.github/workflows/parallel_test.yml
@@ -23,7 +23,7 @@ jobs:
touch Project.toml
julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["MPI", "MPIPreferences"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
julia --project -O3 --check-bounds=no -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'
- julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["Random", "SpecialFunctions", "StatsBase", "Test"]); Pkg.develop(path="moment_kinetics/")'
+ julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["NCDatasets", "Random", "SpecialFunctions", "StatsBase", "Test"]); Pkg.develop(path="moment_kinetics/")'
julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.precompile()'
# Need to use openmpi so that we can use `--oversubscribe` to allow using more MPI ranks than physical cores
./mpiexecjl -np 3 --oversubscribe julia --project -O3 --check-bounds=no moment_kinetics/test/runtests.jl --ci --debug 1
@@ -48,7 +48,7 @@ jobs:
touch Project.toml
julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["MPI", "MPIPreferences"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
julia --project -O3 --check-bounds=no -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'
- julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["Random", "SpecialFunctions", "StatsBase", "Test"]); Pkg.develop(path="moment_kinetics/")'
+ julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["NCDatasets", "Random", "SpecialFunctions", "StatsBase", "Test"]); Pkg.develop(path="moment_kinetics/")'
julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.precompile()'
# Need to use openmpi so that we can use `--oversubscribe` to allow using more MPI ranks than physical cores
./mpiexecjl -np 4 --oversubscribe julia --project -O3 --check-bounds=no moment_kinetics/test/runtests.jl --ci --debug 1
From 2bc99e475d9c2e4a63dc1591cbe0e30a10dc6bcc Mon Sep 17 00:00:00 2001
From: John Omotani <john.omotani@ukaea.uk>
Date: Tue, 8 Oct 2024 14:55:56 +0100
Subject: [PATCH 4/7] Set `parallel_io=false` for a few debug checks
It is good to still test this option even when parallel I/O is
available.
---
moment_kinetics/debug_test/sound_wave_inputs.jl | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/moment_kinetics/debug_test/sound_wave_inputs.jl b/moment_kinetics/debug_test/sound_wave_inputs.jl
index 9f91fa239c..eb1ee45177 100644
--- a/moment_kinetics/debug_test/sound_wave_inputs.jl
+++ b/moment_kinetics/debug_test/sound_wave_inputs.jl
@@ -210,7 +210,8 @@ recursive_merge(test_input_finite_difference_1D1V,
test_input_chebyshev_1D1V_split_1_moment =
recursive_merge(test_input_chebyshev_1D1V,
- OptionsDict("output" => OptionsDict("run_name" => "chebyshev_pseudospectral_1D1V_split_1_moment"),
+ OptionsDict("output" => OptionsDict("run_name" => "chebyshev_pseudospectral_1D1V_split_1_moment",
+ "parallel_io" => false),
"evolve_moments" => OptionsDict("density" => true)))
test_input_chebyshev_1D1V_split_2_moments =
From 219f9bd9a2c1b8797768a3d482d5e7d659e179fd Mon Sep 17 00:00:00 2001
From: John Omotani <john.omotani@ukaea.uk>
Date: Tue, 8 Oct 2024 14:56:38 +0100
Subject: [PATCH 5/7] Test NetCDF I/O in a few debug checks, if available
If NCDatasets is installed (so the NetCDF I/O extension is activated),
then use NetCDF for a few of the debug checks, to test that it is
working properly.
---
moment_kinetics/debug_test/sound_wave_inputs.jl | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/moment_kinetics/debug_test/sound_wave_inputs.jl b/moment_kinetics/debug_test/sound_wave_inputs.jl
index eb1ee45177..3fc8654451 100644
--- a/moment_kinetics/debug_test/sound_wave_inputs.jl
+++ b/moment_kinetics/debug_test/sound_wave_inputs.jl
@@ -1,6 +1,8 @@
test_type = "sound_wave"
using moment_kinetics.type_definitions: OptionsDict
using moment_kinetics.utils: recursive_merge
+using moment_kinetics.file_io: io_has_implementation
+using moment_kinetics.input_structs: netcdf
# default inputs for tests
test_input_finite_difference_1D1V = OptionsDict("output" => OptionsDict("run_name" => "finite_difference_1D1V",
@@ -224,9 +226,13 @@ recursive_merge(test_input_chebyshev_1D1V_split_2_moments,
OptionsDict("output" => OptionsDict("run_name" => "chebyshev_pseudospectral_1D1V_split_3_moments"),
"evolve_moments" => OptionsDict("parallel_pressure" => true)))
+# Use "netcdf" for a few tests to test the NetCDF I/O if it is available.
+const binary_format = io_has_implementation(netcdf) ? "netcdf" : "hdf5"
+
test_input_chebyshev_cx0_1D1V =
recursive_merge(test_input_chebyshev_1D1V,
- OptionsDict("output" => OptionsDict("run_name" => "chebyshev_pseudospectral_cx0_1D1V"),
+ OptionsDict("output" => OptionsDict("run_name" => "chebyshev_pseudospectral_cx0_1D1V",
+ "binary_format" => binary_format),
"reactions" => OptionsDict("charge_exchange_frequency" => 0.0)))
test_input_chebyshev_cx0_1D1V_split_1_moment =
From 399c0941a0d9c600e24a23eb9c3f9eefe0309a88 Mon Sep 17 00:00:00 2001
From: John Omotani <john.omotani@ukaea.uk>
Date: Tue, 8 Oct 2024 17:58:45 +0100
Subject: [PATCH 6/7] Use `--check-bounds=yes` for all commands in
debug_checks.yml
By mistake, one command (creating the `mpiexecjl` executable) was run
with `--check-bounds=no`. This might trigger re-precompilation of
packages, so is inefficient at best.
---
.github/workflows/debug_checks.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.github/workflows/debug_checks.yml b/.github/workflows/debug_checks.yml
index 53c06decf2..e1f4b1f046 100644
--- a/.github/workflows/debug_checks.yml
+++ b/.github/workflows/debug_checks.yml
@@ -29,7 +29,7 @@ jobs:
touch Project.toml
julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.add(["MPI", "MPIPreferences", "PackageCompiler", "NCDatasets", "Symbolics"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
- julia --project -O3 --check-bounds=no -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'
+ julia --project -O3 --check-bounds=yes -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'
julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.develop(path="moment_kinetics/"); Pkg.precompile()'
julia --project -O3 --check-bounds=yes precompile-with-check-bounds.jl --debug 2
From 69faf430be12c2473f2be8cc9d76935a493d572b Mon Sep 17 00:00:00 2001
From: John Omotani <john.omotani@ukaea.uk>
Date: Tue, 8 Oct 2024 18:05:00 +0100
Subject: [PATCH 7/7] Don't install NCDatasets in debug CI job
At the moment installing NCDatasets (and therefore activating the NetCDF
I/O extension) causes precompilation to hang in the debug checks CI job.
Not sure why this is, but skip NCDatasets for now to avoid it.
---
.github/workflows/debug_checks.yml | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/.github/workflows/debug_checks.yml b/.github/workflows/debug_checks.yml
index e1f4b1f046..087407d9b2 100644
--- a/.github/workflows/debug_checks.yml
+++ b/.github/workflows/debug_checks.yml
@@ -28,7 +28,9 @@ jobs:
sed -i -e "s/_debug_level = get_options.*/_debug_level = 2/" moment_kinetics/src/debugging.jl
touch Project.toml
- julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.add(["MPI", "MPIPreferences", "PackageCompiler", "NCDatasets", "Symbolics"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
+ # Not sure why installing "NCDatasets" fails at the moment (8/10/2024), but precompilation hangs for this job if it is included, so skip for now.
+ #julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.add(["MPI", "MPIPreferences", "NCDatasets", "PackageCompiler", "Symbolics"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
+ julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.add(["MPI", "MPIPreferences", "PackageCompiler", "Symbolics"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
julia --project -O3 --check-bounds=yes -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'
julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.develop(path="moment_kinetics/"); Pkg.precompile()'
julia --project -O3 --check-bounds=yes precompile-with-check-bounds.jl --debug 2